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Title :   CRYSTAL STRUCTURE OF P. AERUGINOSA BACTERIOPHYTOCHROME PHOTOSENSORY CORE MODULE MUTANT Q188L IN THE MIXED PR/PFR STATE

Authors :   X. Yang, J. Kuk, K. Moffat

Date :   16 Jul 09 (Deposition) - 22 Sep 09 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.97

Chains :   Asym./Biol. Unit : A,B

Keywords :   Phytochrome, Red-Light Photoreceptor, Photoconversion, Chromophore, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Photoreceptor Protein, Receptor, Sensory Transduction, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Yang, J. Kuk, K. Moffat
Conformational Differences Between The Pfr And Pr States In Pseudomonas Aeruginosa Bacteriophytochrome.
Proc. Natl. Acad. Sci. Usa V. 106 15639 2009
PubMed-ID: 19720999 | Reference-DOI: 10.1073/PNAS.0902178106

Molecule 1 - BACTERIOPHYTOCHROME
	Chains	:	A, B
	EC Number	:	2.7.13.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21/DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET24
	Fragment	:	UNP RESIDUES 1-497
	Gene	:	BPHP, PA4117
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Strain	:	PA01
	Synonym	:	PHYTOCHROME-LIKE PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 24)

No.	Name	Count	Type	Full Name
1	BLA	2	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	22	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:12 , GLU A:15 , ILE A:17 , MSE A:161 , TYR A:163 , TYR A:190 , SER A:193 , ASP A:194 , ILE A:195 , PRO A:196 , TYR A:203 , ARG A:209 , ILE A:211 , ARG A:241 , SER A:244 , HIS A:247 , TYR A:250 , SER A:259 , SER A:261 , SER A:275 , HIS A:277 , PRO A:456 , SER A:459 , HOH A:506	BINDING SITE FOR RESIDUE BLA A 900
2	AC2	SOFTWARE	CYS B:12 , GLU B:15 , MSE B:161 , TYR B:163 , LEU B:188 , TYR B:190 , SER B:193 , ASP B:194 , ILE B:195 , PRO B:196 , ALA B:199 , TYR B:203 , ARG B:209 , ARG B:241 , VAL B:243 , SER B:244 , HIS B:247 , TYR B:250 , SER B:259 , SER B:261 , SER B:275 , HIS B:277 , ARG B:453 , HOH B:506	BINDING SITE FOR RESIDUE BLA B 900

(no "SS Bond" information available for 3IBR)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:222	-	Pro A:223
2	Phe B:222	-	Pro B:223
3	Asp B:393	-	Asn B:394

(no "SAP(SNP)/Variant" information available for 3IBR)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHYTOCHROME_2	PS50046	Phytochrome chromophore attachment site domain profile.	BPHY_PSEAE	139-297	2	A:139-297 B:139-297

(no "Exon" information available for 3IBR)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:457
 aligned with BPHY_PSEAE | Q9HWR3 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:489
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485         
           BPHY_PSEAE     6 PVTLANCEDEPIHVPGAIQPHGALVTLRADGMVLAASENIQALLGFVASPGSYLTQEQVGPEVLRMLEEGLTGNGPWSNSVETRIGEHLFDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHNDTASLLSNVTDELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGQRYPASDIPAQARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNMGVRASMSISIVVGGKLWGLFSCHHMSPKLIPYPVRMSFQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVMLGGRTLSIRGDFERQAGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGGDCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDLMELCL 494
               SCOP domains d3ibra1 A:6-117 Bacteriophytochrome BphP                                                                        d3ibra2 A:118-309 automated matches                                                                                                                                                             d3ibra3 A:310-494 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee.....eeee.....eeeee.hhhhhh..........hhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhh....eeeee......ee.---hhhhhhhh..........eeee...----------....eeeee..-----.eeeeee.....--------------.......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PHYTOCHROME_2  PDB: A:139-297 UniProt: 139-297                                                                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ibr A   6 PVTLANCEDEPIHVPGAIQPHGALVTLRADGmVLAASENIQALLGFVASPGSYLTQEQVGPEVLRmLEEGLTGNGPWSNSVETRIGEHLFDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHNDTASLLSNVTDELRRmTGYDRVmAYRFRHDDSGEVVAESRREDLESYLGLRYPASDIPAQARRLYIQNPIRLIADVAYTPmRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNmGVRASmSISIVVGGKLWGLFSCHHmSPKLIPYPVRmSFQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVmLGGRTLSIR---ERQAGNVLQRLQRDPERDIYHTDNW----------GDCCGVLAIRF-----GWIFWFRHEEVH--------------GPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDLmELCL 494
                                    15        25        35 |      45        55        65     |  75        85        95       105       115       125       135       145       155     | 165       175       185       195       205       215   |   225       235       245       255    |  265       275   |   285    |  295       305       315       325       335       345       355  |    365 |   | 375       385       395         -|      415|     |425       | -         -  |    455       465       475       485    |    
                                                          37-MSE                            71-MSE                                                                            154-MSE  |                                                       219-MSE                            254-MSE |                279-MSE    290-MSE                                                             358-MSE  367 371                     395        406       416   422        433            448                                       490-MSE
                                                                                                                                                                                     161-MSE                                                                                            260-MSE

Chain B from PDB  Type:PROTEIN  Length:457
 aligned with BPHY_PSEAE | Q9HWR3 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:489
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485         
           BPHY_PSEAE     6 PVTLANCEDEPIHVPGAIQPHGALVTLRADGMVLAASENIQALLGFVASPGSYLTQEQVGPEVLRMLEEGLTGNGPWSNSVETRIGEHLFDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHNDTASLLSNVTDELRRMTGYDRVMAYRFRHDDSGEVVAESRREDLESYLGQRYPASDIPAQARRLYIQNPIRLIADVAYTPMRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNMGVRASMSISIVVGGKLWGLFSCHHMSPKLIPYPVRMSFQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVMLGGRTLSIRGDFERQAGNVLQRLQRDPERDIYHTDNWPQPSEDSPDGGDCCGVLAIRFHRQESGWIFWFRHEEVHRIRWGGKPEKLLTIGPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDLMELCL 494
               SCOP domains d3ibrb1 B:6-117 Bacteriophytochrome BphP                                                                        d3ibrb2 B:118-309 automated matches                                                                                                                                                             d3ibrb3 B:310-494 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee...eeeeee.....eeeee.hhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee........eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhh....eeeeee..eeeee.---.hhhhhhhhhhhhh....eeee...----------....eeeee..-----.eeeeee.....--------------.......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------PHYTOCHROME_2  PDB: B:139-297 UniProt: 139-297                                                                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ibr B   6 PVTLANCEDEPIHVPGAIQPHGALVTLRADGmVLAASENIQALLGFVASPGSYLTQEQVGPEVLRmLEEGLTGNGPWSNSVETRIGEHLFDVIGHSYKEVFYLEFEIRTADTLSITSFTLNAQRIIAQVQLHNDTASLLSNVTDELRRmTGYDRVmAYRFRHDDSGEVVAESRREDLESYLGLRYPASDIPAQARRLYIQNPIRLIADVAYTPmRVFPALNPETNESFDLSYSVLRSVSPIHCEYLTNmGVRASmSISIVVGGKLWGLFSCHHmSPKLIPYPVRmSFQIFSQVCSAIVERLEQGRIAELLRVSTERRLALARRARDADDLFGALAHPDDGIAALIPCDGALVmLGGRTLSIR---ERQAGNVLQRLQRDPERDIYHTDNW----------GDCCGVLAIRF-----GWIFWFRHEEVH--------------GPSGPRLTPRGSFEAWEEVVRGHSTPWSETDLAIAEKLRLDLmELCL 494
                                    15        25        35 |      45        55        65     |  75        85        95       105       115       125       135       145       155     | 165       175       185       195       205       215   |   225       235       245       255    |  265       275   |   285    |  295       305       315       325       335       345       355  |    365 |   | 375       385       395         -|      415|     |425       | -         -  |    455       465       475       485    |    
                                                          37-MSE                            71-MSE                                                                            154-MSE  |                                                       219-MSE                            254-MSE |                279-MSE    290-MSE                                                             358-MSE  367 371                     395        406       416   422        433            448                                       490-MSE
                                                                                                                                                                                     161-MSE                                                                                            260-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: automated matches (19)

Protein domain: automated matches (19)

Pseudomonas aeruginosa [TaxId: 287] (2)

1a	d3ibra2	A:118-309
1b	d3ibra3	A:310-494
1c	d3ibrb2	B:118-309
1d	d3ibrb3	B:310-494

Superfamily: PYP-like sensor domain (PAS domain) (163)

Family: BphP N-terminal domain-like (12)

Protein domain: Bacteriophytochrome BphP (10)

Pseudomonas aeruginosa [TaxId: 287] (7)

2a	d3ibra1	A:6-117
2b	d3ibrb1	B:6-117

(no "CATH Domain" information available for 3IBR)

(no "Pfam Domain" information available for 3IBR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BPHY_PSEAE | Q9HWR3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
	GO:0004673	protein histidine kinase activity	Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009584	detection of visible light	The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
	GO:0018106	peptidyl-histidine phosphorylation	The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp B:393 - Asn B:394	[ RasMol ]
		Phe A:222 - Pro A:223	[ RasMol ]
		Phe B:222 - Pro B:223	[ RasMol ]

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	3ibr
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	2.7.13.3
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	BPHY_PSEAE \| Q9HWR3	:	3c2w 3g6o 3nhq 3nop 3not 3nou

Description

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Ligands, Modified Residues, Ions (2, 24)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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